Abstract
Introgression and hybridization are important processes in plant evolution, but they are difficult to study from a phylogenetic perspective, because they conflict with the bifurcating evolutionary history typically depicted in phylogenetic models. The role of hybridization in plant evolution is best documented in the form of allo-polyploidizations. In contrast, homoploid hybridization and introgression are less explored, although they may be crucial in adaptive radiations. Here we employ genome-wide data (ddRAD-seq, transcriptomes) to investigate the evolutionary history of Nepenthes, a radiation of c. 160 species of iconic carnivorous plants mainly from tropical Asia. Our data indicates that the main radiation is only c. 5 million years old, and confirms previous bifurcating phylogenies. However, due to a greatly expanded number of loci, we were able test for the first time the long-standing hypotheses of introgression and historical hybridization. The genus presents one very clear case of organellar capture between two distantly related but sympatric groups. Furthermore, all Nepenthes species show introgression signals in their nuclear genomes, as uncovered by a general survey of ABBA-BABA-like statistics. The ancestor of the rapid main radiation shows ancestry from two deeply diverged lineages, as indicated by phylogenetic network analyses. All major clades of the main radiation show further introgression both within and between each other, as suggested by admixture graphs. Our study supports the hypothesis that rapid adaptive radiations are hotspots of introgression in the tree of life, and highlights the need to consider non-treelike processes in evolutionary studies of Nepenthes in particular.
Highlights
Introgression is emerging as a fundamental process in the diversifi cation of life in general and plants in particular, for example in the form of hybrid speciation or the exchange of genetic variants between species (e.g. Abbott et al, 2013; Folk et al, 2018)
The early diverging grade (EDG) holds N. pervillei from the Seychelles as sister to all other Nepenthes, while all further species with a western distribution branch off sequentially, starting with N. madagascariensis followed by a sister clade of the two species from the Indian subconti nent, N. distillatoria and N. khasiana, N. danseri from Waigeo near New Guinea
Admixture graphs for the remaining eight subsets of taxa are shown in Figure S9 A-H. These results suggested four major admixture events among the main clades of the Nepenthes crown radiation: 1. The tomoriana-group showed a c. 60% genomic contribution from a lineage sister to N. ampullaria or N. mirabilis and N. rafflesiana s.l., and a c. 40% contribution from a lineage diverged at the base of "clade 2"
Summary
Introgression is emerging as a fundamental process in the diversifi cation of life in general and plants in particular, for example in the form of hybrid speciation or the exchange of genetic variants between species (e.g. Abbott et al, 2013; Folk et al, 2018). Discordance or incongruence among gene trees frequently arises from biological processes rather than from methodological arte facts, and it must not be discounted when summarising genomic data into species trees (Degnan and Rosenberg, 2009; Hahn and Nakhleh, 2016; Maddison, 1997). If introgression occurred, it can become apparent as incongruent gene trees with lower evolutionary divergence between species against a baseline of non-introgressed gene trees. The problem is that introgression is just one of several confounding causes of gene tree incongruence
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